Contacts of the helix formed by residues 1091 - 1103 (chain A) in PDB entry 5ID6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU1091 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067A SER* 3.2 30.7 - - - +
1069A GLY 3.7 10.0 + - - +
1070A ASN* 4.2 0.6 - - - +
1071A ARG* 3.5 47.3 - - + +
1089A VAL* 3.7 8.5 + - + +
1090A CYS* 1.3 72.4 - - - +
1092A THR* 1.3 56.1 + - - +
1093A SER 2.6 5.3 + - - -
1094A ALA* 2.3 35.4 + - - +
1095A TYR* 3.2 10.8 + - + -
1130A LEU* 4.3 20.0 - - + +
1133A LEU* 4.5 8.3 - - + -
1134A MSE 3.9 30.7 - - + +
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Residues in contact with THR1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036A TYR* 5.8 0.2 - - - -
1041A ASP* 3.6 16.4 + - - +
1042A LEU* 3.7 18.7 - - + -
1043A PHE* 4.0 11.7 - - - -
1067A SER* 3.5 36.0 - - - +
1068A TYR* 4.5 4.3 - - + +
1069A GLY 4.8 3.1 - - - +
1090A CYS* 5.0 6.3 - - - -
1091A LEU* 1.3 73.3 - - + +
1093A SER* 1.3 54.6 + - - +
1094A ALA 3.4 0.4 - - - -
1095A TYR* 4.0 6.5 - - - -
1096A LYS* 3.5 38.6 + - - +
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Residues in contact with SER1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A CYS* 3.7 28.4 + - - +
1091A LEU 2.6 5.5 + - - -
1092A THR* 1.3 73.6 + - - +
1094A ALA* 1.3 58.8 + - - -
1095A TYR 3.3 0.7 - - - -
1096A LYS* 4.0 11.0 - - - +
1097A GLU* 3.2 27.0 + - - +
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Residues in contact with ALA1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A VAL* 4.2 13.7 - - + -
1090A CYS 3.4 13.5 + - - +
1091A LEU* 2.3 28.5 + - - +
1093A SER* 1.3 69.3 + - - +
1095A TYR* 1.3 56.1 + - - +
1097A GLU* 3.7 6.9 - - - +
1098A LEU* 3.0 28.9 + - - +
1130A LEU* 3.5 26.2 - - + +
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Residues in contact with TYR1095 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A PHE* 3.4 26.2 - + + -
1045A PHE* 3.2 36.9 - + - -
1067A SER* 3.4 26.9 - - - -
1091A LEU* 3.2 18.8 + - + -
1092A THR* 4.0 2.7 - - - +
1094A ALA* 1.3 74.9 - - - +
1096A LYS* 1.3 68.0 + - - +
1098A LEU* 3.2 3.3 + - + +
1099A PHE* 2.9 53.2 + + + -
1127A PHE* 4.5 12.6 - + - -
1130A LEU* 3.4 37.4 - - + +
1131A MSE 4.0 18.0 - - + +
1134A MSE 3.9 12.4 - - - +
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Residues in contact with LYS1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036A TYR* 3.8 21.4 + - - -
1041A ASP* 2.4 40.4 + - - -
1043A PHE* 3.9 5.5 - - + -
1092A THR* 3.5 24.0 + - - +
1093A SER* 4.0 8.5 - - - +
1095A TYR* 1.3 77.0 - - - +
1097A GLU* 1.3 60.2 + - - +
1099A PHE 3.6 0.2 + - - -
1100A ASN* 2.7 37.7 + - - +
1106A TYR* 3.3 37.4 - - + +
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Residues in contact with GLU1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A SER* 3.2 18.8 + - - +
1094A ALA* 3.7 8.0 - - - +
1095A TYR 3.2 0.2 - - - -
1096A LYS* 1.3 81.3 - - - +
1098A LEU* 1.3 62.1 + - + +
1100A ASN* 3.1 8.0 + - - +
1101A LYS* 2.8 32.6 + - + +
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Residues in contact with LEU1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A ALA 3.0 15.7 + - - +
1095A TYR* 3.2 3.8 + - - +
1097A GLU* 1.3 81.6 - - + +
1099A PHE* 1.3 65.9 + - + +
1101A LYS* 3.2 25.1 - - + +
1102A TYR* 3.2 36.1 + - + +
1104A ILE* 5.0 0.3 - - - +
1123A PHE* 4.3 10.3 - - + +
1126A SER* 3.1 36.3 - - - +
1127A PHE* 3.8 24.0 - - + +
1130A LEU* 3.9 15.3 - - + -
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Residues in contact with PHE1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034A ILE* 5.7 2.7 - - + -
1043A PHE* 3.6 28.0 - + - -
1045A PHE* 5.8 0.7 - + - -
1095A TYR* 2.9 48.0 + + + +
1098A LEU* 1.3 78.2 - - + +
1100A ASN* 1.3 66.5 + - - +
1102A TYR 3.1 6.1 + - - -
1104A ILE* 2.8 53.5 + - + +
1106A TYR* 3.5 35.7 - + + -
1111A ILE* 4.3 13.5 - - + -
1115A LEU* 4.0 17.5 - - + -
1123A PHE* 4.5 6.3 - + - -
1127A PHE* 4.4 22.2 - + - -
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Residues in contact with ASN1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A LYS* 2.7 28.4 + - - +
1097A GLU* 3.1 9.6 + - - +
1099A PHE* 1.3 73.6 - - - +
1101A LYS* 1.3 64.8 + - - +
1102A TYR 3.0 1.6 + - - -
1103A GLY* 3.0 13.6 + - - -
1104A ILE 4.7 3.5 - - - +
1105A ASN* 5.6 2.1 - - - +
1106A TYR* 3.6 24.1 + - - -
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Residues in contact with LYS1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097A GLU* 2.8 18.2 + - + +
1098A LEU* 3.2 25.1 - - + +
1099A PHE 3.2 0.2 - - - -
1100A ASN* 1.3 76.6 - - - +
1102A TYR* 1.3 91.7 + - + +
1103A GLY 3.8 0.3 + - - -
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Residues in contact with TYR1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098A LEU* 3.2 36.0 + - + +
1099A PHE 3.1 3.2 + - - -
1100A ASN 3.0 0.8 + - - -
1101A LYS* 1.3 111.9 + - + +
1103A GLY* 1.3 62.1 + - - +
1104A ILE* 3.3 21.7 + - + -
1118A GLN* 3.8 28.9 + - - +
1120A ASP* 4.0 20.2 - - - -
1122A ALA* 3.1 30.1 + - - +
1123A PHE* 3.8 31.4 - + + -
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Residues in contact with GLY1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100A ASN* 3.0 14.5 + - - -
1101A LYS 3.5 0.8 + - - -
1102A TYR* 1.3 79.1 - - - +
1104A ILE* 1.3 60.9 + - - +
1105A ASN* 3.7 7.8 + - - +
1114A LEU* 5.7 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il